Installation error: error: could not find szip

[emilyluisedoyle]

Hi,

I have been running into a consistent error trying to download the rGEDI package using

devtools::install_git("https://github.com/carlos-alberto-silva/rGEDI", dependencies = TRUE)

A similar issue was raised last month (https://github.com/carlos-alberto-silva/rGEDI/issues/38) and I have followed the solutions but to no avail. The error message is as follows:

configure: error: could not find szip: Debian: sudo apt install libsz2 RPM-based: sudo dnf install szip MacOS: brew install szip ERROR: configuration failed for package ‘rGEDI’ removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/rGEDI’ Warning message: In i.p(...) : installation of package ‘/var/folders/yg/zvz4kc0x2mv6mm_vm5t_s7dr0000gp/T//Rtmpea8Weh/file23eb11acef3f/rGEDI_0.3.0.tar.gz’ had non-zero exit status

Also to note, szip is not available in the brew library so instead I tried:

brew install libzip

however this still does not work and the szip error remains. I used Macports to successfully install szip in the terminal but the error still remains.

I am using macOS Monterey 12.4 on an M1 (with arm64mac) and R version 4.2.1. Hopefully its an easy fix - look forward to hearing from you! Thank you

[caiohamamura]

Unfortunately I don't have a Mac machine to test, but the GitHub's Workflow using Mac is working fine. The system requirements are installed in a single line:

brew install libzip hdf5 gdal gsl automake

[Xitermelon]

Hello, I have exactly the same problem. I tried "brew install libzip hdf5 gdal gsl automake" but the error still remains.

[caiohamamura]

Sorry, but we do not have access to Mac machine, we are only using automated workflow to check MacOS installation, see https://github.com/carlos-alberto-silva/rGEDI/blob/master/.github/workflows/r.yml#L77, from line 77-80 the only custom command for compiling in MacOS is:

brew install libzip hdf5 gdal gsl automake

[Xitermelon]

Somehow it doesn't work for Mac, still "could not find szip", but the development version works on Windows now.

[caiohamamura]

As a workaround you could try to ignore the szip checking part. Open a terminal prompt and then:

1. Clone the repository git clone https://github.com/carlos-alberto-silva/rGEDI
2. Change to the rGEDI directory: cd rGEDI
3. Initialize submodule git submodule init
4. Update submodules git submodule update
5. Edit the configure.ac file and remove lines 41-49 which are checking for szip.
6. Install autoconf: brew install autoconf
7. Run autoreconf: autoreconf
8. Run R or RStudio in the rGEDI directory and then run: devtools::install()

If this works please let us know and we try some workaround for macOS szip checking.

You can try to run everything from this:

git clone https://github.com/carlos-alberto-silva/rGEDI
cd rGEDI
git submodule update --init
sed -i .bak -e '41,51d' configure.ac
sudo brew install autoconf
autoreconf
Rscript -e "devtools::install()"

[ajs0428]

As a workaround you could try to ignore the szip checking part. Open a terminal prompt and then:

1. Clone the repository `git clone https://github.com/carlos-alberto-silva/rGEDI`

2. Change to the rGEDI directory: `cd rGEDI`

3. Initialize submodule `git submodule init`

4. Update submodules `git submodule update`

5. Edit the `configure.ac` file and remove lines 41-49 which are checking for szip.

6. Install autoconf: `brew install autoconf`

7. Run autoreconf: `autoreconf`

8. Run R or RStudio in the rGEDI directory and then run: `devtools::install()`

If this works please let us know and we try some workaround for macOS szip checking.

You can try to run everything from this:

git clone https://github.com/carlos-alberto-silva/rGEDI
cd rGEDI
git submodule update --init
sed -i .bak -e '41,51d' configure.ac
sudo brew install autoconf
autoreconf
Rscript -e "devtools::install()"

Apologies since this was marked closed but I just tried this on MacOS Ventura R version 4.3.0 and wasn't able to install still. Any additional help would be much appreciated

[caiohamamura]

And what was the error?

[ajs0428]

I was able to replicate the error within just the terminal which is shown in the images below. But I just tried again this time using devtools::install and setting the path to the recently updated rGEDI package folder within RStudio and it worked. Not sure what the difference and any insight is appreciated

[caiohamamura]

Unfortunately this must be something to do with incompatible versions of libhdf5 installed in your system, as it is being reported with other different softwares such as https://github.com/ranganathanlab/bmDCA/issues/2. As I don't have a Mac machine for testing I cannot help you further. Maybe you could have better luck asking about it in some forum dedicated for superusers/MacOS experts, or the Apple support per se.

The github link I provided has some instructions you could try to see if they work.

The relevant error message is Library not loaded @rpath/libhdf5.200.dylib, as you can see this has nothing to do with rGEDI, as the package is only using libhdf5 as a dependency. It looks like the linker (which we do not have much control over) is trying to use a version that is different from the one found by /Users/Anthony/opt/miniconda3/bin/h5cc binary utility.

It looks like it is trying to use the libhdf5 from miniconda3 you installed previously. As a workaround you could try to use R from the miniconda's R package, or try to get rid of miniconda3 at all because it looks like it is conflicting with your R environment.

[ajs0428]

Thanks! I'll look into some MacOS specific issues with the libhdf5. Also will probably just get rid of miniconda, odd that it's stuck using that version.